A5072996397- Advanced Proteomics Techniques and Applications
- RNA and protein synthesis mechanisms
- Mass Spectrometry Techniques and Applications
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Molecular Biology Techniques and Applications
- Genetic and phenotypic traits in livestock
- RNA modifications and cancer
- Metabolomics and Mass Spectrometry Studies
- Antimicrobial Peptides and Activities
- Glycosylation and Glycoproteins Research
- Ubiquitin and proteasome pathways
- Genetic Mapping and Diversity in Plants and Animals
- Genomics and Chromatin Dynamics
- Cancer-related molecular mechanisms research
- Herpesvirus Infections and Treatments
- Wheat and Barley Genetics and Pathology
- Veterinary Equine Medical Research
- Peptidase Inhibition and Analysis
- Esophageal Cancer Research and Treatment
- Atrial Fibrillation Management and Outcomes
- Yeasts and Rust Fungi Studies
- Peanut Plant Research Studies
- Animal Virus Infections Studies
- Muscle Physiology and Disorders
Sun Yat-sen Memorial Hospital
2024
Sun Yat-sen University
2024
Sichuan University
2024
King's College London
2023
Tibet Academy of Agricultural and Animal Husbandry Sciences
2020
Chinese Academy of Agricultural Sciences
2009-2018
BGI Group (China)
2012-2018
China National GeneBank
2016
King Abdulaziz University
2014
Chinese Academy of Sciences
2014
Peptide identification based upon mass spectrometry (MS) is generally achieved by comparison of the experimental spectra with theoretically digested peptides derived from a reference protein database. Obviously, this strategy could not identify peptide and sequences that are absent A customized database on basis RNA-Seq data thus proposed to assist improve novel peptides. Correspondingly, development comprehensive pipeline, which provides an end-to-end solution for detection database,...
Investigations of missing proteins (MPs) are being endorsed by many bioanalytical strategies. We proposed that proteogenomics testis tissue was a feasible approach to identify more MPs because tissues have higher gene expression levels. Here we combined proteomics and transcriptomics survey in human from three post-mortem individuals. Proteins were extracted separated with glycine- tricine-SDS-PAGE. A total 9597 protein groups identified; these, 166 listed as MPs, including 138 (83.1%)...
We propose an efficient integration of SWATH with MRM for biomarker discovery and verification when the corresponding ion library is well established. strictly controlled false positive rate associated MS signals carefully selected target peptides coupled MRM. collected 10 samples esophageal squamous cell carcinoma (ESCC) tissues paired tumors adjacent regions quantified 1758 unique proteins FDR 1% at protein level using SWATH, in which 467 were abundance-dependent ESCC. After evaluating...
Liquid chromatography coupled tandem mass spectrometry (LC-MS/MS) is an important technique for detecting peptides in proteomics studies. Here, we present open source software tool, termed IPeak, a peptide identification pipeline that designed to combine the Percolator post-processing algorithm and multi-search strategy enhance sensitivity of identifications without compromising accuracy. IPeak provides graphical user interface (GUI) as well command-line interface, which implemented JAVA can...
The strategy of sequential window acquisition all theoretical fragment ion spectra (SWATH) is emerging in the field label-free proteomics. A critical consideration for processing SWATH data quality library (or mass spectrometric reference map). As availability open spectral libraries that can be used to process limited, most users currently create their in-house. Herein, we propose an approach construct expanded using data-dependent (DDA) generated by fractionation We identified three...
Toll-like receptor 2 (TLR2) plays an important role in the innate immune response to a variety of pathogens. In this study, bovine TLR2 gene was taken as candidate for mastitis resistance. Through PCR-SSCP analysis and sequencing, three missense mutations at T385 G, G398A, G1884A were detected coding region that encoded extracellular domain. Altogether 240 dairy cattle breeds (Holstein, Simmental, Sanhe cattle) genotyped allele frequencies determined. The effects polymorphisms on somatic...
Human Proteome Project (HPP) aims at mapping entire human proteins with a systematic effort upon all the emerging techniques, which would enhance understanding of biology and lay foundation for development medical applications. Until now, 2563 missing (MPs, PE2-4) are still undetected even using most sensitive approach protein detection. Herein, we propose that enrichment low-abundance benefits MPs finding. ProteoMiner is an equalizing technique by reducing high-abundance enriching in...
Abstract Background Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is one of the primary crops cultivated in mountains Tibet and encounters low temperature, high salinity, drought. Specifically, drought major abiotic stresses that affect limit growth. Osmotic stress often simultaneously accompanied by conditions. Thus, to improve crop yield, it critical explore molecular mechanism governing responses osmotic/drought Findings In this study, we used quantitative proteomics...
A multiple-mouse solenoidal MR coil was developed for in vivo imaging of up to 13 mice simultaneously screen tumors on a 1.5 T clinical scanner. For the be effective as screening tool, it should permit acquisition MRIs which orthotopic with diameters >2 mm are detectable reasonable period time (<1 hr magnet time) and their sizes accurately measured. Using spin echo sequence, we demonstrated that this provides sufficient sensitivity moderately high resolution images (156-176 microm...
Abstract Summary: Single nucleotide variations (SNVs) located within a reading frame can result in single amino acid polymorphisms (SAPs), leading to alteration of the corresponding sequence as well function protein. Accurate detection SAPs is an important issue proteomic analysis at experimental and bioinformatic level. Herein, we present sapFinder, R software package, for variant peptides based on tandem mass spectrometry (MS/MS)-based proteomics data. This package automates construction...
Rice (Oryza sativa) is one of the most important worldwide crops. The genome has been available for over 10 years and undergone several rounds annotation. We created a comprehensive database transcripts from 29 public RNA sequencing data sets, officially predicted genes Ensembl plants, common contaminants in which to search protein-level evidence. re-analyzed nine publicly accessible rice proteomics sets. In total, we identified 420K peptide spectrum matches 47K peptides 8,187 protein...
Our first proteomic exploration of human chromosome 1 began in 2012 (CCPD 1.0), and the genome-wide characterization proteome through public resources revealed that 32–39% proteins on remain unidentified. To characterize all missing proteins, we applied an OMICS-integrated analysis three liver cell lines (Hep3B, MHCC97H, HCCLM3) using mRNA ribosome nascent-chain complex-bound deep sequencing profiling, contributing mass spectrometric evidence 60 additional gene products. Integration...
Stroke is a serious global public health issue, associated with severe disability and high mortality rates. Its early detection challenging, no effective biomarkers are available. To obtain better understanding of stroke prevention, management, recovery, we conducted lipidomic analyses to characterize plasma metabolic features. Lipid species were measured using an untargeted analysis liquid chromatography-tandem mass spectrometry. Sixty participants recruited in this cohort study, including...
Linkage disequilibrium (LD) plays an important role in genomic selection and mapping quantitative trait loci (QTL). In this study, the pattern of LD effective population size (Ne ) were investigated Chinese beef Simmental cattle. A total 640 bulls genotyped with IlluminaBovinSNP50BeadChip IlluminaBovinHDBeadChip. We estimated for each autosomal chromosome at distance between two random SNPs <0 to 25 kb, 50 100 500 0.5 1 Mb, 5 Mb 10 Mb. The mean values r(2) 0.30, 0.16 0.08, when separation...
Under the guidance of Chromosome-centric Human Proteome Project (C-HPP),(1, 2) we conducted a systematic survey expression status genes located at human chromosome 20 (Chr.20) in three cancer tissues, gastric, colon, and liver carcinoma, their representative cell lines. We have globally profiled proteomes these samples with combined technology LC–MS/MS acquired corresponding mRNA information upon RNA-seq RNAchip. In total, 323 unique proteins were identified, covering 60% coding (323/547)...
Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing-You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined many species recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the mechanisms underlying beak deformity, we performed genome-wide CNV detection using Affymetrix high-density 600K data on...
A priority in solving the problem of drug resistance is to understand molecular mechanism how a induces response within cells. Because many cancer cells exhibit chromosome aneuploidy, we explored whether changes aneuploidy status result resistance. Two typical colorectal cells, HCT116 and LoVo, were cultured with chemotherapeutic drugs irinotecan (SN38) or oxaliplatin (QxPt), non- drug-resistant cell lines selected. Whole exome sequencing (WES) was employed evaluate these RNAseq LC-MS/MS...
Cancer genomics unveils many cancer-related mutations, including some chromosome 20 (Chr.20) genes. The mutated messages have been found in the corresponding mRNAs; however, whether they could be translated to proteins still requires more evidence. Herein, we proposed a transomics strategy profile expression status of human Chr.20 genes (555 Ensembl v72). data transcriptome and translatome (the mRNAs bound with ribosome, translating mRNAs) revealed that ∼80% coding on were detected mRNA...
Chromosome 8, a medium-length euchromatic unit in humans that has an extraordinarily high mutation rate, can be detected not only evolution but also multiple mutant diseases, such as tumorigenesis, and further invasion/metastasis. The Chromosome-Centric Human Proteome Project of China systematically profiles the proteomes three digestive organs (i.e., stomach, colon, liver) their corresponding carcinoma tissues/cell lines according to chromosome organizational roadmap. By rigorous standards,...
Myogenic determination factor 1 (MyoD1) and myogenic 6 (Myf6) genes belong to the differentiation (MyoD) gene family, which play key roles in growth muscle development. The study aimed investigate effects of variants cattle MyoD1 Myf6 on carcass meat traits. We screened single nucleotide polymorphisms (SNPs) both 8 populations, including Simmental, Angus, Hereford, Charolais, Limousin, Qinchuan, Luxi, Jinnan by sequencing. G782A locus was identified exon (MyoD1-BglI) as well T186C...
Accurate predictions of peptide retention times (RT) in liquid chromatography have many applications mass spectrometry-based proteomics. Herein, we present DeepRT, a deep learning based software for time prediction. DeepRT automatically learns features directly from the sequences using convolutional Neural Network (CNN) and Recurrent (RNN) model, which eliminates need to use hand-crafted or rules. After feature learning, principal component analysis (PCA) was used dimensionality reduction,...
SNPs in 5ꞌ-flanking region of the bovine TG gene that gene-specific may be a useful marker for growth traits marker-assisted selection programs beef cattle.
Thinopyrum intermedium carries many useful traits for wheat genetic improvement. To identify genes conferring resistance to stripe rust caused by Puccinia striiformis f. sp. tritici in Zhong4, one of the Zhong series partial amphiploids from hybrids common × Th. intermedium, a cross was made between Zhong4 and Chinese Spring ph1b mutant (CS-ph1b). The parents, F 1 , 2 plants 5 lines were tested with predominant race CYR31 P. seedling stage under controlled greenhouse conditions. Of 201...
β-Defensins (DEFBs) have a variety of functions. The majority these proteins were not identified in recent proteome survey. Neither protein detection nor the analysis transcriptomic data based on RNA-seq for three liver cancer cell lines any expression products. Extensive investigation into DEFB transcripts over 70 offered similar results. This fact naturally begs question—Why are genes scarcely expressed? After examining gene annotation and physicochemical properties its products, we...